Cloning, Purification and Characterization of the Collagenase ColA Expressed by Bacillus cereus ATCC 14579
Cloning, Purification and Characterization of the Collagenase ColA Expressed by Bacillus cereus ATCC 14579
Carmen M. Abfalter 0 1
Esther Schönauer 1
Karthe Ponnuraj 1
Markus Huemer 0 1
Gabriele Gadermaier 1
Christof Regl 1
Peter Briza 1
Fatima Ferreira 1
Christian G. Huber 1
Hans Brandstetter 1
Gernot Posselt 0 1
Silja Wessler 0 1
0 Department of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg , Salzburg , Austria , 2 Department of Molecular Biology, Division of Structural Biology, Paris-Lodron University of Salzburg , Salzburg , Austria , 3 Centre of Advanced Study in Crystallography and Biophysics, University of Madras , Guindy Campus, Chennai , India , 4 Department of Molecular Biology, Division of Allergy and Immunology, Paris-Lodron University of Salzburg , Salzburg , Austria , 5 Department of Molecular Biology, Division of Chemistry and Bioanalytics, Paris-Lodron University of Salzburg , Salzburg , Austria
1 Editor: Xianwu Cheng, Nagoya University , JAPAN
Bacterial collagenases differ considerably in their structure and functions. The collagenases ColH and ColG from Clostridium histolyticum and ColA expressed by Clostridium perfringens are well-characterized collagenases that cleave triple-helical collagen, which were therefore termed as ´true´ collagenases. ColA from Bacillus cereus (B. cereus) has been added to the collection of true collagenases. However, the molecular characteristics of B. cereus ColA are less understood. In this study, we identified ColA as a secreted true collagenase from B. cereus ATCC 14579, which is transcriptionally controlled by the regulon phospholipase C regulator (PlcR). B. cereus ATCC 14579 ColA was cloned to express recombinant wildtype ColA (ColAwt) and mutated to a proteolytically inactive (ColAE501A) version. Recombinant ColAwt was tested for gelatinolytic and collagenolytic activities and ColAE501A was used for the production of a polyclonal anti-ColA antibody. Comparison of ColAwt activity with homologous proteases in additional strains of B. cereus sensu lato (B. cereus s.l.) and related clostridial collagenases revealed that B. cereus ATCC 14579 ColA is a highly active peptidolytic and collagenolytic protease. These findings could lead to a deeper insight into the function and mechanism of bacterial collagenases which are used in medical and biotechnological applications.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information files.
Funding: The authors received no specific funding
for this work.
Competing Interests: The authors have declared
that no competing interests exist.
Collagen is the most abundant component of the extracellular matrix (ECM) in vertebrates,
which provides not only a flexible scaffold for embedded cells, but also regulates crucially
important cellular processes including differentiation, cellular growth, survival, migration, and
many more [
]. Dynamic remodeling of the ECM constantly requires redistributions,
modifications and also degradation of ECM components to maintain functional tissue
]. Numerous collagenases have been described as non-specific or
pseudocollagenases. Pseudocollagenases degrade gelatin or non-helical regions of collagen, while only true
collagenases can cleave triple-helical regions within the three chains of native collagen .
Both types of proteases are strongly associated with diseases like metastasis of tumors,
inflammation, ulceration, rheumatoid arthritis or bacterial infections [
]. Examples for
pseudocollagenases are mammalian tissue enzymes like pepsin, trypsin, chymotrypsin or papain. The
group of true collagenases includes selected members of the matrix metalloprotease family
(MMP-1, -8, -13, -14) and cathepsin K which contribute to ECM proteolysis [
Additionally, bacterial collagenases can interfere with collagen functions in the ECM. Pathogens such as
Borrelia burgdorferi, Peptostreptococcus magnus, Vibrio alginolyticus, Achromobacter lyticus,
Porphyromonas gingivalis, Treponema denticola, Streptococcus gordnii, etc. express collagenases
belonging to the group of metalloproteases, serine proteases or thiol proteases . In particular,
collagenases expressed by Clostridium histolyticum constitute well characterized paradigms
which are, together with additional proteases and toxins, implicated in clostridial-dependent
Clostridial ColH and ColG have been described as zinc-dependent metalloproteases that
contain an N-terminal signal peptide, a putative propeptide, an activator domain followed by
the catalytic peptidase domain, one or two polycystic kidney disease-like domain (PKD)
domains, and one to three collagen binding domains (CBD) [
]. As members of the
gluzincin subfamily, clostridial collagenases bind the catalytic zinc ion via the two histidine residues
in the consensus HEXXH sequence in the active center; a third zinc ligand is provided by a
glutamate approximately 33–35 amino acids downstream of the HEXXH motif . Structural
data are available for the catalytic domains of ColG and ColH from C. histolyticum and ColT
from C. tetani revealing a double glycine motif upstream of the HEXXH motif, which is also
necessary for the collagenase activity [
]. Upon calcium binding the PKD-like domain of
ColG undergoes a conformational domain rearrangement [
]. Both, zinc and calcium
binding is required for full proteolytic activity [
]. In a proposed two-state model of ColG, collagen
recognition, binding and cleavage involve an opened and closed ColG conformation [
indicating a coordinated mechanism in collagenase function. The preferred cleavage sites cover the
typical collagen motifs Gly-Pro-X and Gly-X-Hyp (hydroxyproline) [
Besides Clostridia, collagenolytic and gelatinolytic activities have also been observed in
several bacterial species of Bacillus cereus s.l. (i.e. B. cereus sensu stricto [B. cereus s.s.], B. mycoides,
B. pseudomycoides, B. thuringiensis, B. weihenstephanensis, B. anthracis and B. cytotoxicus [
], which are less characterized. B. cereus s.s. and its closely related family members are
Gram-positive, spore forming and facultative anaerobic bacteria ubiquitously found in the
environment. As an opportunistic bacterium, B. cereus s.s. has been identified as an increasing
cause of food-borne diseases leading to gastrointestinal disorders, but also of
non-gastrointestinal diseases in patients [
]. B. cereus pathogenicity is associated with the expression of
several toxins and virulence factors. Among them, hemolysins, phospholipase C, emetic toxin,
proteases or enterotoxins have been connected to the induction of gastrointestinal and
nongastrointestinal diseases, such as endophthalmitis [
], wound infections [
] or rare
cases of postoperative meningitis [
] and pneumonia [
]. Most of these factors are
regulated by the pleiotropic regulon phospholipase C regulator (PlcR) . PlcR-regulates
gene expression via a conserved palindromic sequence in the promotor regions of its target
]. B. cereus also expresses collagenases in a PlcR-dependent manner , which
might contribute to bacterial pathogenesis through the degradation of collagen in the ECM.
For instance, it was suggested that collagenases facilitate B. cereus invasion into the eye lens
and thus promote bacterial endophthalmitis [
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Studies on B. cereus collagenase activity were exclusively performed using secreted
collagenase(s) enriched from supernatants of bacterial liquid cultures [
]. Comparable to
clostridial collagenases, it was demonstrated that B. cereus collagenase activity is zinc-dependent,
could be induced by calcium ions , and targets native collagen [
]. However, detailed
biochemical analyses have not been performed so far.
In a previous study, we have detected gelatinolytic activities of B. cereus ATCC 14579 in
zymography analyses and which are strongly active in the logarithmic growth phase [
obtain deeper insights into the molecular functions of the collagenolytic B. cereus proteases, we
identified the endogenously expressed collagenase and analyzed recombinant ColA acting as a
highly active and secreted true collagenase from B. cereus ATCC 14579.
Materials and Methods
Bacillus cereus (ATCC 14579) and Bacillus thuringiensis (strain 407) were obtained from Nalini
Ramarao (INRA, La Minière, Guyancourt, France). The B. cereus ATCC 14579 deletion mutant
lacking the plcR regulon (BcΔplcR) was a kind gift from Michel Gohar (INRA, Génétique
Microbienne et Environnement Jouy-en-Josas, France). Bacillus subtilis (DSM 402), Bacillus
weihenstephanensis and Bacillus megaterium were included as further controls. All bacteria
were grown in brain heart infusion (BHI) medium (Sigma Aldrich) at 37°C overnight shaking
at 200 rpm. Overnight cultures were diluted 1:20 in fresh BHI medium and bacteria and their
corresponding supernatants from the liquid cultures were harvested after indicated time
periods by centrifugation at 3000 x g for 10 min at 4°C. Supernatants were sterile-filtered (0.22 nm
filter, Greiner). Bacterial pellets were resuspended in lysis buffer (20 mM Tris pH 7.5, 100 mM
NaCl, 1% Triton X-100, 0.5% DOC, 0.1% SDS, 0.5% NP-40) and sonicated 3 x for 30 sec with
50% power [
]. Bacterial lysates were cleared from debris by centrifugation at 16000 x g for 10
min at 4°C and protein amounts were determined by Bradford protein assay (Carl Roth).
Supernatants of B. cereus ATCC 14579 were loaded on a preparative gelatin zymogram as
described before [
]. Briefly, transparent bands were excised from the zymogram and proteins
were electro-eluted using D-Tube™ Dialyzer Midi (Merck Millipore). After concentrating using
Centricon1 (Merck Millipore), the protein samples were separated via SDS-PAGE. To
visualize the proteins, gels were stained using 1% Coomassie Brilliant Blue G250 (BioRad). Protein
bands were excised and digested with the ProteoExtract All-in-One Trypsin Digestion Kit
(Merck Millipore). Resulting peptides were separated by reverse-phase nano-HPLC (Dionex
Ultimate 3000, Thermo Fisher Scientific). Peptides were loaded onto the trap column (PepSwift
Monolithic Trap Column, Dionex) and desalted with 0.1% (v/v) heptafluorobutyric acid at a
flow rate of 10 μl/min. After 5 minutes, trap and separation column (PepSwift Monolithic
Nano Column, 100 μm x 25 cm, Dionex) were coupled with a switching valve and the peptides
were eluted with an acetonitrile gradient (Solvent A: 0.1% (v/v) FA/0.01% (v/v) TFA/5% (v/v)
ACN; solvent B: 0.1% (v/v) FA/0.01% (v/v) TFA/90% (v/v) ACN; 5–45% B in 60 min) at flow
rate of 1 μl/min at 55°C. The HPLC was directly coupled via nano electrospray to a Q-Exactive
Orbitrap mass spectrometer (Thermo Fisher Scientific). Capillary voltage was 2 kV. For
peptide identification, a top 12 method was used with the normalized fragmentation energy at
27%. For protein identification, Proteome Discoverer version 1.4 (Thermo Fisher Scientific)
with SequestHD and UniProtKB was used.
To analyze the cleavage site of the GST-ColA ΔSP, the GST fragment was precipitated using
glutathione sepharose. After elution, the samples were diluted in 0.1% (v/v) aqueous formic
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a accession number;
b restriction recognition sites are underlined;
c substituted nucleotides are underlined
acid to a final concentration of 0.1 mg/ml. Intra-molecular disulfide bonds were reduced with 5
mM TCEP (Sigma-Aldrich Chemie GmbH) at 60°C for 30 minutes. The analysis was carried
out on a high-performance liquid chromatography (HPLC) system (Ultimate 3000, Thermo
Fisher Scientific) at a flow rate of 200 μl/min. A Supelco Discovery C18 column (150 × 2.1 mm
i.d., 3 μm particle size, 300 Å pore size, Sigma-Aldrich) was operated at a column temperature
of 50°C. 10 μl of sample were injected in in-line split-loop mode. Separation was carried out
with a gradient of 5.0–50.0% (v/v) acetonitrile (ACN, VWR) in 0.1% (v/v) formic acid (FA,
Sigma-Aldrich Chemie GmbH) in 20 min, followed by column regeneration at 99.99% ACN in
0.1% FA for 10 min and re-equilibration at 5.0% in 0.1% FA for 15 min. UV-detection was
carried out with a 2.5 μl flow-cell at 214 nm. Mass spectrometry was conducted on a
quadrupoleOrbitrap instrument (QExactive) equipped with an Ion Max source with a heated electrospray
ionization (HESI) probe from Thermo Fisher Scientific. Mass calibration of the instrument
was conducted with Pierce™ LTQ Velos ESI Positive Ion Calibration Solution from Life
Technologies. The instrument settings were as follows: source heater temperature of 200°C, spray
voltage of 4.0 kV, sheath gas flow of 15 arbitrary units, auxiliary gas flow of 5 arbitrary units,
capillary temperature of 300°C, S-lens RF level of 60.0, in-source CID of 20.0 eV, AGC target
of 1e6 and a maximum injection time of 200 ms. The intact protein measurements were carried
out in full scan mode with a range of m/z 1,000–2,500 at a resolution of 140,000 at m/z 200.
Deconvolution of the intact ion spectra was carried out with the Xtract algorithm integrated
into the software Xcalibur 3.0.63 (Thermo Fisher Scientific).
Cloning, Mutagenesis and Purification of ColA
The collagenase ColA (BC3161, Gene ID: 1205508) was amplified from bacterial genomic
DNA from B. cereus strain ATCC 14579. PCR primers (Table 1) were designed to amplify
ColA lacking the predicted signal peptide (ColA ΔSP, aa 31–960) or lacking the predicted
propeptide (ColA ΔPP, aa 93–960). The amplified BamHI/XhoI flanked PCR products were cloned
into the pGEX-6P-1 plasmid (GE Healthcare Life Sciences) and transformed in E. coli BL21 to
create a GST-ColA fusion protein. To generate a protease-inactive ColA protein, glutamic acid
501 was substituted by an alanine (ColAE501A) (primers in Table 1) using the QuikChange
Lightning Site-Directed Mutagenesis Kit (Agilent) according to the manufacturer’s
instructions. For heterologous expression and purification of ColA proteins, transformed E. coli was
grown in 300 ml LB medium to an OD600 of 0.5–0.7 at 37°C and 200 rpm and the expression
was induced by the addition of 0.1 mM isopropylthiogalactosid (IPTG) at 30°C for 3 h. The
bacterial culture was pelleted at 4500 x g for 30 minutes and bacteria were lysed in 10 ml
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cold PBS by sonication. The lysate was cleared by centrifugation and the supernatant was
incubated with glutathione sepharose (GE Healthcare Life Sciences) at 4°C overnight as described
]. The fusion protein was either eluted with 10 mM reduced glutathione for 10
minutes at room temperature or cleaved with 180 U Prescission Protease for 16 h at 4°C (GE
Healthcare Life Sciences).
Bacterial lysates, supernatants or recombinant proteins were separated by SDS-PAGE
containing 0.1% gelatin under non reducing conditions as described previously [
separated by the gels were renatured (2.5% TritonX-100) for 1 h, incubated in developing buffer
(50 mM Tris pH 7.5, 200 mM NaCl, 5 mM CaCl2, 0.02% Brij35) for 16 hours at 37°C and
stained using 0.5% Coomassie Brilliant Blue R250 (BioRad).
SDS-PAGE and Western Blot
Proteins were separated by SDS-PAGE under reducing conditions and stained using 1%
Coomassie Brilliant Blue G250 (BioRad). For Western blot analyses, equal amounts of proteins
were separated by SDS-PAGE and blotted on PVDF membranes. B. cereus ATCC 14579 ColA
was detected using a polyclonal anti-ColA antiserum produced in rabbits immunized with
recombinant ColA ΔPPE501A (Davids Biotechnology, Germany). To detect the GST-tag, an
anti-GST antibody (Rockland) was applied. Visualizing was performed using Odyssey1 Fc
Imaging System (LiCor).
In Vitro Cleavage Assays
Enzymatic assays with N-[3-(2-Furyl)acryloyl]-Leu-Gly-Pro-Ala (FALGPA) as substrate were
performed as described by van Wart and Steinbrink [
] and detailed in the manufacturer’s
protocol (AppliChem) with some minor modifications. Briefly, ColA ΔPPwt or ColA ΔPPE501A
were incubated with FALGPA in 250 mM Hepes, 10 mM CaCl2, 10 mM ZnCl2. Collagenase G
from Clostridium histolyticum (ColG) (Q9X721; Y119-K1118) and the peptidase domain of C.
tetani ColT (ColTPD) (Q899Y1, D340-K731) were used as controls [
]. The enzymes were
analyzed at 0.67 μM using a substrate concentration of 2 mM FALPGA in 60 μL reaction volume.
The concentration of FALGPA was verified in solution via UV absorbance at 305 nm (ε305 =
24.70 mM-1 cm-1). All measurements were performed at 25°C, and the decrease in absorbance
upon substrate cleavage was monitored at 345 nm in 1 min intervals for 25 min with an Infinite
M200 plate reader (Tecan). Complete substrate turnover (100%) was accomplished by ColTPD
and ColA ΔPPwt after 20 min. All experiments were performed in triplicates and repeated three
times. Ratio of substrate turnover (+/- SD) was calculated normalized on the lowest substrate
absorbance measured. Significance was calculated using Student´s t-test (paired, one tailed)
with a significance threshold of p < 0.05 (GraphPad Prism 5).
For the collagenolytic assays, pepsin-extracted soluble type I collagen from bovine skin (Cell
Guidance Systems Ltd) was used at a final concentration of 1 mg/ml (i.e. 3.33 μM assuming a
molecular mass of 300 kDa, corresponding to non-polymerized tropocollagen) in 250 mM
Hepes pH 7.5, 150 mM sodium chloride, 5 mM calcium chloride and 5 μM zinc chloride. The
collagen was incubated with 0.83 μM alpha-chymotrypsin (Sigma-Aldrich) and 0.055 μM
ColG, ColTPD, ColA ΔPPwt and ColA ΔPPE501A at 25°C. Samples were taken at the indicated
time points and the reactions were stopped with 10 mM copper chloride for
alpha-chymotrypsin, and with 50 mM EDTA for the other proteins. To test whether ColA targets additional
proteins from the ECM, 1 μg ColA ΔPP was incubated with 1 μg fibrinogen (Bovine Plasma,
Calbiochem), 1 μg human vitronectin (R&D), 1 μg laminin (mouse, BD Bioscience), 1 μg
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collagen (Sigma) or 5 μg casein (Carl Roth) in 50 mM HEPES pH 7.4 or collagenase cleavage
buffer containing 50 mM Tris, 500 mM NaCl, 20 mM CaCl2, pH 7.6 for 16 hours at 37°C.
The full length amino acid sequence of B. cereus ATCC 14579 ColA (Q81BJ6) was used as a
target sequence to search for templates using BLASTp against the protein data bank (PDB)
] as well as the SWISS-MODEL server [
]. Among the templates obtained from
the SWISS-MODEL, the 2.5 Å crystal structure of apo collagenase G (ColG) from C.
histolyticum (PDB 2Y3U) was considered as the most suitable candidate to model the residues
Y93-K850 of B. cereus ATCC 14579 ColA. A sequence identity of 49.80% was observed
between the corresponding regions of B. cereus ATCC 14579 ColA and C. histolyticum ColG
proteins. The quality of the obtained model (Y93-K850) was evaluated by RAMPAGE [
The electrostatic potential surface of both ColA and ColG was generated using the program
PyMOL (The PyMOL Molecular Graphics System, Version 1.7.4 Schrodinger, LLC).
Bacterial Species of Bacillus cereus s.l. Express Gelatinolytic Proteases
In a previous study, we detected a gelatinolytic protease in B. cereus ATCC 14579 [
analyze whether also other species from the B. cereus s.l. group and additional Bacillus species
express similar active proteases, gelatinolytic activities in lysates of B. subtilis, B. megaterium, B.
thuringiensis and B. weihenstephanensis were compared with B. cereus ATCC 14579 in gelatin
zymography. Equal protein amounts of B. subtilis (Bs), B. megaterium (Bm), B. thuringiensis (Bt),
B. weihenstephanensis (Bw) and B. cereus ATCC 14579 (Bc) lysates were separated in a gelatin
zymogram (Fig 1A). Transparent bands in the coomassie-stained gel refer to an active protease
cleaving gelatin. As described previously [
], we detected active proteases in a B. cereus ATCC
14579 lysate with molecular weights between 80 kDa and 110 kDa (Fig 1A, lane 5). A similar
protease pattern was also identified in a lysate of B. thuringiensis (Fig 1A, lane 3). In the lysate of B.
weihenstephanensis, we observed a predominant proteolytic activity at a molecular weight of 120
kDa (Fig 1A, lane 4). In contrast, the lysate of B. subtilis showed a different activity pattern with
two distinct bands at 55 kDa and 35 kDa (Fig 1A, lane 1). In B. megaterium, no activity was
detectable (Fig 1A, lane 2). In order to control equal protein yield of the bacterial cultures, all
lysates were analyzed by SDS PAGE and stained with coomassie brilliant blue (Fig 1B). To
identify the gelatinolytic protease of B. cereus ATCC 14579, we performed a preparative zymogram,
electro-eluted the proteins from the excised gel and analyzed the proteins by coomassie-stained
SDS PAGEs. Excised proteins were finally examined by mass-spectrometry. Among several
protein hits, two peptides of the collagenase ColT (bcere0001_4490) from B. cereus m1293 were
identified that correspond to the orthologous collagenase ColA (BC_3161) from B. cereus strain
ATCC 14579 exhibiting 76.8% identity (Table 2) in the N-terminus (S1 Fig).
Cloning and Purification of Recombinant B. cereus ATCC 14579 ColA
The domain structure of ColG from C. histolyticum covers an activator domain, peptidase
domain, a PKD domain, and the two CBD domains alpha and beta. In comparison to ColG,
clostridial ColH harbors a second PKD domain, but only one CBD domain [
of B. cereus ColA (Q81BJ6, gene name: BC_3161) with ColH (Q46085) and ColG (Q9X721)
revealed a slightly higher identity of ColA to ColG (44.77%) than to ColH (44.15%) (S2 Fig).
Web based resources SMART (simple modular architecture research tool, http://smart.
embl.de/) and SignalP (SignalP4.1, http://www.cbs.dtu.dk/services/SignalP/) [
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Fig 1. Gelatinolytic activities expressed by different Bacillus species. (A) Equal amounts of proteins in lysates of B. subtilis (Bs), B.
megaterium (Bm), B. thuringiensis (Bt), B. weihenstephanensis (Bw) and B. cereus ATCC 14579 (Bc) were analyzed for proteolytic activity in
gelatin zymography. Protein standard (m) indicated molecular weights of gelatinolytic activities. (B) Efficient disruption of bacteria and equal
protein amounts were demonstrated by coomassie-stained SDS PAGEs. Protein standard (m) indicated molecular weights of proteins.
a signal peptide (aa 1–30) and a propeptide in the N-terminus of ColA (aa 31–92) (Figs 2A and
S2 Fig). The analysis further suggested a M9 peptidase domain (aa 93–634), a PKD domain (aa
770–852) and a prepeptidase c-terminal (PPC) domain (aa 880–947), which corresponds to
the CBD domain of ColG (S2 Fig).
According to the predicted domain architecture, B. cereus ATCC 14579 ColA variants
lacking the putative signal peptide (ColA ΔSP) or also the predicted propeptide (ColA ΔPP) were
cloned and overexpressed in E. coli to purify ColA ΔSP and ColA ΔPP as N-terminally tagged
GST-ColA fusion proteins (Fig 2A). Lysates of E. coli transformed with expression constructs
for GST-ColA ΔSPwt were analyzed by coomassie-stained SDS PAGE (S3A Fig, lane 1).
GST-ColA ΔSPwt, which had a predicted molecular weight of approximately 132.8 kDa was not
observed, but appeared to be processed into a ~100 kDa protein and a 26 kDa GST protein as
detected by SDS PAGE (S3A Fig). The identity of GST was also confirmed by Western blotting
(S3A Fig, lanes 9–12). To analyze whether an autoproteolytic processing of GST-ColA ΔSPwt
Collagenase family protein
7 / 19
Fig 2. Cloning, overexpression and activity of B. cereus ATCC 14579 ColA. (A) ColA is expressed as a 110.1 kDa protein
and consists of a 3.3 kDa signal peptide (aa 1–30), a 7.2 kDa propetide (aa 31–92) and a 99.6 kDa C-terminal part (aa 93–960) of
ColA. Expression constructs for N-terminally GST-tagged ColA ΔSP (132.8 kDa) and ColA ΔPP (125.6 kDa) were cloned.
Glutamic acid (E) 501 in the active center of ColA was exchanged by an alanine (E501A) to create proteolytically inactive ColA.
(B) The expression, enrichment and activity of GST-ColA ΔPPwt and GST-ColA ΔPPE501A proteins in IPTG-induced E. coli
lysates or purified via GST pull down (PD) experiments were analyzed by SDS-PAGE (left panel) and gelatin zymography
(middle panel). To purify ColA ΔPPwt, transformed E. coli (-) were induced by IPTG to stimulate GST-ColA ΔPPwt expression.
After lysing bacteria, GST-ColA ΔPPwt was bound to GST sepharose and either eluted by glutathione (PD) as a GST fusion
protein (GST-ColA ΔPPwt) or cleaved and eluted with the PreScission protease (PreSc) to obtain the untagged protease ColA
8 / 19
occurred, a protease-inactive variant was created by the exchange of the glutamic acid 501 to
an alanine in the active center (ColA ΔSPE501A). In contrast to GST-ColA ΔSPwt in bacterial
lysates, proteolytic-inactive GST-ColA ΔSPE501A migrated with the predicted molecular weight
of approximately 132.8 kDa (S3A Fig, lane 2). In GST pull-down (PD) experiments with
GST-ColA ΔSPwt, only the 26 kDa GST tag could be enriched, while the GST-ColA ΔSPE501A
samples yielded the 132.8 kDa full length protein (S3A Fig, lanes 3–4). Furthermore, the
gelatinolytic activities of these proteins were analyzed by zymography. GST-ColA ΔSP is
gelatinolytically active, but exhibited a lower molecular weight in the range of 100 kDa than the expected
132.8 kDa (S3A Fig, lane 5, asterisk). The GST-ColA ΔSPE501A mutant was proteolytically
inactive (S3A Fig, lanes 6 and 8). Together, these data indicate that the N-terminal GST tag of ColA
ΔSP was autocatalytically removed.
Subsequently, we generated isogenic GST-ColA ΔPPwt and its inactive GST-ColA ΔPPE501A
mutant for the further characterization of recombinant B. cereus ATCC 14579 ColA (Fig 2A
and 2B). GST-tagged proteins lacking the propeptide exhibited the predicted molecular weight
of 125.6 kDa and were detected in the lysates of IPTG-induced E. coli (Fig 2B, lanes 1–2) and in
GST-PD experiments (Fig 2B, lanes 3–4). Comparing the molecular weight of autoprocessed
GST-ColA ΔSPwt in E. coli lysates (S3B Fig, lane 7) with the different recombinant protein
variants GST-ColA ΔSPE501A (132.8 kDa), ColA ΔSPE501A (106.8 kDa), GST-ColA ΔPPwt (125.6
kDa), ColA ΔPPwt (99.6 kDa), GST-ColA ΔPPE501A (125.6 kDa) and ColA ΔPPE501A (99.6
kDa) (S3B Fig) showed that the autoprocessed GST-ColA ΔSPwt migrated at the size of the
106.8 kDa ColA ΔSPE501A protein. This indicated that ColAwt cleaves off the GST tag, but not
the propeptide and could further indicate that ColA cleaves-off its signal peptide in an
autocatalytic manner. Therefore, we aimed to identify the cleavage site by mass-spectrometry analyses
of the processed GST tag. These analyses revealed that ColA cleaves in the amino acid stretch
FQ#GPL in the linker between the GST tag and ColA ΔSPwt protein (S4 Fig).
For further analyses of the proteolytic activity of ColA, we finally expressed GST-ColA
ΔPPwt protein in E. coli. In contrast to the inactive GST-ColA ΔPPE501A mutant (Fig 2B, lanes 6
and 8), GST-ColA ΔPPwt proteins were gelatinolytic active in zymography analyses (Fig 2B,
lanes 5 and 7). Both, induction and enrichment of GST-ColA ΔPPwt protein were analyzed by
coomassie-stained SDS PAGEs (Fig 2B, lanes 9–11). To remove the GST tag from the fusion
protein, GST-ColA ΔPPwt coupled to GST sepharose was incubated with PreScission protease
resulting in the release of ColA ΔPPwt (Fig 2B, lane 12).
Recombinant B. cereus ATCC 14579 ColA Acts as a True Collagenase
To examine the peptidase activity of recombinant ColA ΔPPwt from B. cereus ATCC 14579 in
more detail, N-[3-(2-Furyl)acryloyl]-Leu-Gly-Pro-Ala (FALGPA) was used as a synthetic
peptide-substrate mimicking the consensus collagenase cleavage site. We compared the activity of
the B. cereus ATCC 14579 ColA ΔPPwt with the recombinant protease domain of ColT from C.
tetani (ColTPD) [
]. Proteolytic inactive ColA ΔPPE501A and ColG from C. histolyticum
exhibiting low peptidolytic activity [
] were included as negative controls. Incubation of FALGPA
with ColA ΔPPwt led to a rapid substrate turnover of ~85% after 12 min, which was comparable
with the activity of ColTPD (Fig 3A).
To further analyze the collagenolytic activity, we tested collagenases on their ability to cleave
tropocollagen I composed of the β, α1 and α2 chains (Fig 3B, lanes 1 and 6). Incubation of
tropocollagen with ColG induced a slight fragmentation of tropocollagen after 6 h, which
drastically increased after 24 h (Fig 3B, lanes 2–5). A strong fragmentation of tropocollagen was
observed after incubation of tropocollagen with ColA ΔPPwt as no collagen was detectable after
24 h (Fig 3B, lanes 7–10). This underlines that ColA from B. cereus ATCC 14579 targets not
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Fig 3. Collagenolytic activity of ColA. (A) ColA ΔPP from B. cereus ATCC 14579, its inactive version ColA ΔPPE501A, ColG from C. histolyticum and
the protease domain of ColT (ColTPD) from C. tetani were tested for their peptidase activity using FALGPA as a substrate. * p = 0.0161 indicates
statistical significance (Student´s t-test, paired, one-tailed). (B) In in vitro cleavage assays, the positive control ColG and ColA ΔPPwt were incubated
with tropocollagen type I for the indicated time periods and analyzed by coomassie stained SDS PAGE to analyze their collagenolytic activities. (C) As
negative controls, ColTPD and ColAΔPPE501A were investigated. (D) As indicated, α–chymotrypsin was incubated with tropocollagen type I as an
additional negative control and compared to untreated tropocollagen type I for the indicated time periods and analyzed by coomassie stained SDS
only denatured collagen, but efficiently cleaves tropocollagen and thus can be considered as a
true collagenase. Most likely, ColA is the main collagenolytic entity described in B. cereus
]. In contrast, the peptidase domain of ColTPD which lacked the activator
domain, and the inactive ColA ΔPPE501A did not cleave tropocollagen (Fig 3C), similar to
chymotrypsin which only induced a limited cleavage of collagen (Fig 3D). These data underline
the finding that ColA expressed by B. cereus ATCC 14579 can target native collagen. ColA
activity appeared highly specific as we did not identify further substrates from the ECM, such
as laminin and fibrinogen (S5A Fig) or vitronectin (S5B Fig). Casein was included as an
additional protease substrate (S5B Fig).
In comparison with ColG, B. cereus ATCC 14579 ColA is exceptionally active. However, a
crystal structure of B. cereus ATCC 14579 ColA is not available yet, which could explain the
increased activity. Therefore, comparative protein modelling was used to model the residues
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Fig 4. Homology model of B. cereus ATCC 14579 ColA and the comparison of the surface property of ColA and ColG from C. histolyticum
near the catalytic site. (A) Ribbon representation of modeled collagenase module of B. cereus ATCC 14579 ColA, which consists of an N-terminal
activator domain (green) followed by a catalytic subdomain (cyan) and a C-terminal catalytic helper subdomain (grey). Electrostatic surface potential of
collagenase module of (B) B. cereus ATCC 14579 ColA and (C) C. histolyticum ColG (PDB 2Y3U). The basic and acidic regions are shown in blue and
Y93-K850 of B. cereus ATCC 14579 ColA, which comprises the activator domain, a catalytic
subdomain and a catalytic helper subdomain (Fig 4A). The quality of the obtained model
(Y93K850) was evaluated by RAMPAGE [
] and 95.8% of the modeled residues are present in the
favored region, 3.1% of them are in the allowed region and 1.0% residues are outliers. Based on
this homology model, the electrostatic surface potential of B. cereus ATCC 14579 ColA was
calculated and compared to ColG (Fig 4B and 4C). Interestingly, this analysis revealed that the
surface properties of ColA and ColG at the activator domain (Fig 4B and 4C, dotted lines)
differed significantly. ColA exhibited a highly basic surface, whereas the corresponding region in
ColG was acidic, which might potentially explain the difference in their activities.
B. cereus ATCC 14579 ColA Expression Is Under Control of the plcR
Based on the finding that both endogenous and recombinant ColA are highly active and true
collagenases, we analyzed the activities of collagenases in bacterial lysates and supernatants of
B. cereus ATCC 14579 wildtype (wt) and an isogenic plcR deletion mutant (ΔplcR). B. cereus
ATCC 14579 strains were cultured in BHI medium and after indicated time periods, equal
amounts of bacterial lysates and supernatants were analyzed for collagenase activity in gelatin
11 / 19
zymography. As a control, recombinant ColA ΔPPwt (rColA) was included (Fig 5, lane 9). In
fact, we observed several gelatinolytic activities in the lysates of B. cereus ATCC 14579 wt (Fig
5, lanes 1–4, upper panel). To correlate the observed activity with ColA expression, we
generated a polyclonal anti-ColA antibody raised against rColA (ColA ΔPPE501A). We detected ColA
protein in bacterial lysates in Western blot analysis (S6 Fig), which corresponds to gelatinolytic
activities (Fig 5, upper panel). ColA activity was increased at 2 h and 4 h and decreased again at
8 h post-inoculation. Only a weak activity was observed in the plcR deletion mutant (Fig 5,
lanes 5–8, upper panel) indicating that ColA is regulated by the plcR regulon as described
]. Collagenase activities appeared at least at four different molecular weights
suggesting that multiple ColA variants were present (Fig 5, upper panel). The intensity of the
individual proteolytic activities was slightly changed in the culture supernatants at different
growth phases (Fig 5, middle panel). Here, we detected three main activities, which increased
at 2 h and 4 h of culture. The activity with the highest molecular weight decreased at 8 h, while
the activity of intermediate size increased (Fig 5, lanes 1–4, middle panel). The identity of
secreted ColA was further validated by Western blot analysis (Fig 5, lower panel). Our data
suggest that ColA processing occurs during secretion, which could be substantiated by the
detection of different ColA versions in Western blot analyses (Fig 5, lower panel). In
comparison with 99.6 kDa rColA, the largest secreted ColA version from B. cereus ATCC 14579
migrates at the same molecular weight (Fig 5, lanes 1–4). Putative cleavage products were
produced, which can result from N-terminally, but also from C-terminal processing as described
for ColG .
Bacterial proteases are often directly or indirectly related to their virulence as they can either
interfere directly with host cell functions or are involved in the processing of other bacterial
virulence factors [
]. Collagenases attracted special attention since they can hydrolyze
collagen, which represents an important structural component of the ECM. For instance, the
collagenase of V. vulnificus has been described to promote bacterial invasion into human tissue
]. Helicobacter pylori expresses the collagenase Hp0169, which was demonstrated to be
an essential factor for bacterial colonization of the murine stomach [
]. Similar roles have
been suggested for clostridial collagenases indicating the importance of bacterial collagenases
in microbial pathogenesis [
]. In the last decades, clostridial collagenases also have been
applied in safe and efficient therapeutic intervention strategies for Peyronie's or Dupuytren
]. Hence, intensive research on clostridial proteases increased the knowledge on
structure, activity and function of collagenases. However, less is known about collagenases
expressed by B. cereus s.l. In our previous work, we observed a highly active collagenase
expressed by B. cereus ATCC 14579 [
], which has been reported as a collagenase in the
supernatants of B. cereus s.s. in earlier studies [
], but was not further characterized. In
this study we provide evidence that the described gelatinolytic activity is the true collagenase
ColA secreted by B. cereus ATCC 14579, and which targets helical collagen.
Collagenases from Clostridia were described as zinc-dependent metalloproteases composed
of an N-terminal signal peptide, a putative propeptide, an activator domain followed by the
catalytic peptidase domain, and a varying number of PKD and CBD domains [
domain architecture and structure have been intensively investigated revealing the molecular
mechanisms of true collagenases [
]. Corresponding to previous reports [
], ColA also
acts as a true collagenase, which targets gelatin, FALGPA and native tropocollagen type I,
indicating that ColA prefers the typical collagen motifs Gly-Pro-X and Gly-X-Hyp [
] as cleavage
sites. In comparison with the collagenase paradigm ColG from C. histolyticum, B. cereus ATCC
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Fig 5. ColA is secreted by B. cereus ATCC 14579. B. cereus ATCC 14579 wildtype (wt) and its isogenic
ΔplcR deletion mutant were harvested and disrupted after growing in liquid cultures for indicated time
periods. Equal protein amounts of bacterial lysates (upper panel) and equal volumes of supernatants were
analyzed by gelatin zymography (upper and middle panel) and Western blotting using a polyclonal antibody
directed against ColA ΔPPE501A (lower panel). Recombinant ColA ΔPP (rColA) was used as control.
13 / 19
14579 ColA exhibited a fast enzymatic degradation of tropocollagen. Analyzing structural
differences, a homology model of the collagenase activator and peptidase domains of B. cereus
ColA points to alterations of the surface charge of ColA and ColG that could possibly explain
the different enzymatic activities. This feature might play a significant role in collagen
recognition and binding and could help to explain the difference in the activities of these two proteases.
B. cereus collagenase has previously been described as a secreted protease [
we mainly observed two proteolytic activities in supernatants of B. cereus ATCC 14579.
Although we cannot exclude the possibility that additional collagenases were expressed in B.
cereus, our data suggest that ColA processing occurs during secretion, which could be
substantiated by the detection of different ColA variants in Western blot analyses. Since the size of
secreted ColA matched the size of recombinant ColA ΔPP, we assume that secreted ColA lacks
not only the signal peptide, but also the propeptide. As the maturation of ColA was not
investigated in this study, it remains unknown if ColA is a self-processing protease or if additional
proteases are implicated in ColA secretion. In fact, several functions have been proposed for
Nterminally located signal peptides and propeptides in Gram-positive and Gram-negative
bacteria. It was suggested that propeptides are required for proper folding, for secretion of the
mature protease, for maintaining the protease in an inactive state, or for anchoring the protease
to the membrane [
]. N-terminal cleavage and conversion from the proform of the protease
into an active form was already described for other well characterized metalloproteases like for
] and for trypsin-like proteases [
]. For the metalloprotease Npr of Streptomyces
cacaoi, it has been proposed that the signal peptide directs Npr to the membrane. After removal
of the signal peptide, Npr is released into the environment, where the propeptide is cleaved-off
]. According to our data, the secreted B. cereus ColA did not contain the propeptide,
therefore we assume that the removal of the signal peptide and propeptide is involved in ColA
secretion via a yet unknown mechanism. Additional processing of ColA in bacterial
supernatants was observed, which could reflect C-terminal cleavage events as already proposed for
other collagenases [
7, 13, 57
]. However, the molecular consequences of ColA cleavage on the
protease function needs to be investigated in future studies.
Many virulence factors of B. cereus are controlled by the transcriptional regulator PlcR [
via binding to the PlcR box upstream of regulated target genes [
]. Described as a
pleiotropic regulator, PlcR can control the expression of a wide range of virulence-associated genes
including enterotoxins, cytotoxins, and hemolysins . Here, we observed that ColA
expression is down-regulated in a plcR-negative B. cereus mutant, which is in line with a previous
study that mapped a PlcR box upstream of the bc3161 gene in the B. cereus ATCC 14579 strain
]. Transcription of PlcR is increased in bacteria at the beginning of the stationary growth
], which correlates with PlcR-controlled expression of secreted B. cereus factors [
This is in contrast to another report suggesting a decrease of the plcR transcript and
PlcR-controlled nhe and hbl expression in the stationary growth phase of the anaerobic B. cereus F4430/
]. Although we did not analyze the PlcR expression in B. cereus ATCC 14579 in our
experiments under aerobic conditions, we conclude that PlcR-dependent ColA expression and
secretion already start in the logarithmic growth phase [
In conclusion, we identified ColA as the major secreted true collagenase of B. cereus ATCC
14579. The existence of additional orthologs to the colA gene bc_3161 in other sequenced B.
cereus sensu stricto strains as well as B. cereus group strains (Table 2) implies that expression of
bacilli collagenase is a wide spread phenomenon and needs to be investigated in future. Cloning
and purification of recombinant ColA revealed that it is a highly active protease that efficiently
targets native tropocollagen. Furthermore, it might contribute to bacterial virulence of B. cereus
in endophthalmitis or opportunistic infections via collagen degradation in the ECM. Clostridial
collagenases already represent a widespread compound in the treatment of several diseases,
14 / 19
such as Peyronie's or Dupuytren diseases. The high activity of B. cereus ColA makes it an
additional attractive candidate for medical treatments.
S1 Fig. Alignment of ColT from B. cereus m1293 and ColA from B. cereus ATCC 14579.
Protein sequences from B. cereus m1293 ColT and B. cereus Bc3161 were retrieved from
UniProt. Sequence alignments were performed using Clustal Omega. ( ) indicates identical amino
acids in all sequences, conserved amino acid substitutions are labeled with (:) and
semi-conservative substitutions are marked with (.).
S2 Fig. Alignment of ColA from B. cereus, ColH from C. histolyticum and ColG from C.
histolyticum. ColG from C. histolyticum harbors an activator domain (green), peptidase domain
(blue), a PKD domain (yellow), and the two CBD domains alpha (grey), and beta (dark grey).
ColH harbors a second PKD domain, but only one CBD domain. Sequence analysis revealed
that ColA from B. cereus contains a signal peptide (aa 1–30, black box) and predicted a
propeptide in the N-terminus of ColA (aa 31–92, red box). A M9 peptidase domain (aa 93–634), is
followed by a PKD domain (aa 770–852) and a prepeptidase c-terminal (PPC) or CBD domain
S3 Fig. Expression of ColA ΔSP and ColA ΔPP proteins. (A) GST-ColA ΔSPwt and
GST-ColA ΔSPE501A proteins in lysates or precipitated by GST pull down (PD) experiments
were analyzed by SDS-PAGE (left panel), by gelatin zymography (middle panel), and by
Western blot analysis using a polyclonal antibody directed against GST (right panel). (B) 1 μg of
tested proteins after GST-PD experiments was separated by SDS PAGE and stained using
coomassie. Where indicated the GST tag was removed by the PreScission protease. The protein
standard (m) shows the actual size of proteins in the coomassie-stained gel (on the left) in
comparison to the theoretical molecular weight as indicated on the right (lanes 1–8). Lysates of
induced E. coli transformed with the expression plasmid encoding the GST-ColA ΔSPwt were
included to verify the molecular weight of the processed protein (lane 9).
S4 Fig. Intact mass spectrum of reduced GST-ColA ΔSP (a) and GST fragment (b). Mass
spectrometry revealed that the cleavage site is C-terminal to Q226 at the LFQ/GPL motif.
Deconvolution of the intact ion spectra was carried out with the Xtract algorithm integrated
into the software Xcalibur 3.0.63 (Thermo Fisher Scientific).
S5 Fig. Substrate selectivity of ColA. The putative substrates laminin (1 μg), fibrinogen
(1 μg), collagen (1 μg) (A) or vitronectin (1 μg) and casein (5 μg) (B) were incubated with 1 μg
ColA or left untreated (-) for 16 hours. Proteins were separated by SDS PAGE followed by
S6 Fig. Detection of ColA in the lysates of B. cereus. Equal protein amounts of bacterial
lysates of B. cereus ATCC 14579 grown for indicated time periods were analyzed by Western
blotting. The polyclonal anti-ColA antibody detected endogenous ColA. An unspecific
crossreactivity has been indicated by an asterisk ( ). Recombinant ColA ΔPPwt (rColA) served as a
15 / 19
We thank Michel Gohar, Didier Lereclus and Nalini Ramarao for providing bacterial strains
and are grateful to Isabel J. Hoppe for providing ColG protein. This work was supported by the
publication funds of the University of Salzburg.
Conceptualization: GP SW.
Data curation: CMA ES.
Formal analysis: CMA ES KP.
Funding acquisition: SW.
Methodology: CMA GP SW.
Project administration: SW.
Resources: CH HB FF KP.
Supervision: GP SW.
Validation: CMA GP SW.
Investigation: CMA ES KP MH GG PB CR.
Visualization: CMA MH CR ES KP.
Writing – original draft: CMA SW.
Writing – review & editing: CMA GP SW.
16 / 19
17 / 19
official publication of the European Society of Clinical Microbiology. 2004; 23(9):725–8. Epub 2004/08/
10. doi: 10.1007/s10096-004-1180-y PMID: 15300457.
18 / 19
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